Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization.

Colorectal cancer (CRC) is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can develop via distinct pathways where metastasis is the primary cause of death. Therefore, it is crucial to understand the molecular mechanisms underlying metastasis. RNA-sequencing is an essential tool used for studying the transcriptional landscape. However, the high-dimensionality of gene expression data makes selecting novel metastatic biomarkers problematic. To distinguish early-stage CRC patients at risk of developing metastasis from those that are not, three types of binary classification approaches were used: (1) classification methods (decision trees, linear and radial kernel support vector machines, logistic regression, and random forest) using differentially expressed genes (DEGs) as input features; (2) regularized logistic regression based on the Elastic Net penalty and the proposed iTwiner-a network-based regularizer accounting for gene correlation information; and (3) classification methods based on the genes pre-selected using regularized logistic regression. Classifiers using the DEGs as features showed similar results, with random forest showing the highest accuracy. Using regularized logistic regression on the full dataset yielded no improvement in the methods' accuracy. Further classification using the pre-selected genes found by different penalty factors, instead of the DEGs, significantly improved the accuracy of the binary classifiers. Moreover, the use of network-based correlation information (iTwiner) for gene selection produced the best classification results and the identification of more stable and robust gene sets. Some are known to be tumor suppressor genes (OPCML-IT2), to be related to resistance to cancer therapies (RAC1P3), or to be involved in several cancer processes such as genome stability (XRCC6P2), tumor growth and metastasis (MIR602) and regulation of gene transcription (NME2P2). We show that the classification of CRC patients based on pre-selected features by regularized logistic regression is a valuable alternative to using DEGs, significantly increasing the models' predictive performance. Moreover, the use of correlation-based penalization for biomarker selection stands as a promising strategy for predicting patients' groups based on RNA-seq data.

HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome.

Colorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.

Low doses of ionizing radiation activate endothelial cells and induce angiogenesis in peritumoral tissues.

PURPOSE: During radiotherapy the peritumoral tissues are daily exposed to subtherapeutic doses of ionizing radiation. Herein, the biological and molecular effects of doses lower than 0.8 Gy per fraction (LDIR), previously described as angiogenesis inducers, were assessed in human peritumoral tissues. MATERIAL AND METHODS: Paired biopsies of preperitoneal adipose tissue were surgically collected from 16 patients diagnosed with locally advanced rectal cancer who underwent neo-adjuvant radiotherapy. One of the biopsies is located in the vicinity of the region where the tumor received the prescribed dose of radiation, and thus exposed to LDIR; the other specimen, outside all beam apertures, was used as an internal calibrator (IC). Microvessel density (MDV) was quantified by immunohistochemistry and the expression of angiogenic, pro-inflammatory, adhesion and oxidative stress genes was assessed by quantitative RT-PCR using exclusively endothelial cells (ECs) isolated by laser capture microdissection microscopy. RESULTS: LDIR activated peritumoral ECs by significantly up-regulating the expression of several pro-angiogenic genes such as VEGFR1, VEGFR2, ANGPT2, TGFB2, VWF, FGF2, HGF and PDGFC and down-regulating the pro-inflammatory IL8 marker. Accordingly, the MVD was significantly increased in peritumoral tissues exposed to LDIR, compared to the IC. The patients that yielded a larger pro-angiogenic response, also showed the highest MVD. CONCLUSIONS: LDIR activate ECs in peritumoral tissues that are associated with increased MVD. Although the technological advances in radiotherapy have contributed to reduce the damage to healthy tissues over the past years, the anatomical regions receiving LDIR should be taken into account in the treatment plan report for patient follow-up and in future studies to correlate these doses with tumor dissemination.

Low doses of ionizing radiation activate endothelial cells and induce angiogenesis in peritumoral tissues.

PURPOSE: During radiotherapy the peritumoral tissues are daily exposed to subtherapeutic doses of ionizing radiation. Herein, the biological and molecular effects of doses lower than 0.8 Gy per fraction (LDIR), previously described as angiogenesis inducers, were assessed in human peritumoral tissues. MATERIAL AND METHODS: Paired biopsies of preperitoneal adipose tissue were surgically collected from 16 patients diagnosed with locally advanced rectal cancer who underwent neo-adjuvant radiotherapy. One of the biopsies is located in the vicinity of the region where the tumor received the prescribed dose of radiation, and thus exposed to LDIR; the other specimen, outside all beam apertures, was used as an internal calibrator (IC). Microvessel density (MDV) was quantified by immunohistochemistry and the expression of several pro-angiogenic genes was assessed by quantitative RT-PCR using exclusively endothelial cells (ECs) isolated by laser capture microdissection microscopy. RESULTS: LDIR activated peritumoral ECs by significantly up-regulating the expression of several pro-angiogenic genes such as VEGFR1, VEGFR2, ANGPT2, TGFB2, VWF, FGF2, HGF and PDGFC. Accordingly, the MVD was significantly increased in peritumoral tissues exposed to LDIR, compared to the IC. The patients that yielded a larger pro-angiogenic response, also showed the highest MVD. CONCLUSIONS: LDIR activate ECs in peritumoral tissues that are associated with increased MVD. Although the technological advances in radiotherapy have contributed to reduce the damage to healthy tissues over the past years, the anatomical regions receiving LDIR should be taken into account in the treatment plan report for patient follow-up and in future studies to correlate these doses with tumor dissemination.

Electrodeposition of indium from the ionic liquid trihexyl(tetradecyl)phosphonium chloride.

The electrochemical behavior of indium in the ionic liquid trihexyl(tetradecyl)phosphonium chloride (Cyphos IL 101) was studied. Cyphos IL 101 first had to be purified, as the impurities present in commercial Cyphos IL 101 interfered with the electrochemical measurements. Electrochemical deposition of indium metal from this electrolyte occurs without hydrogen evolution, increasing the cathodic current efficiency compared to deposition from water and avoiding porosity within the deposited metal. Indium(iii) is the most stable oxidation state in the ionic liquid. This ion is reduced in two steps, first from indium(iii) to indium(i) and subsequently to indium(0). The high thermal stability of Cyphos IL 101 allowed the electrodeposition of indium at 120 °C and 180 °C. At 180 °C indium was deposited as liquid indium which allows for the easy separation of the indium and the possibility to design a continuous electrowinning process. On molybdenum, indium deposits as liquid droplets even below the melting point of indium. This was explained by the combination of melting point depression and undercooling. The possibility to separate indium from iron and zinc by electrodeposition was tested. It is possible to separate indium from zinc by electrodeposition, but iron deposits together with indium.

Cobalt(ii) containing liquid metal salts for electrodeposition of cobalt and electrochemical nanoparticle formation.

Cobalt(ii)-containing liquid metal salts (LMS) with N-alkylimidazole ligands and bis(trifluoromethanesulfonyl)imide (bistriflimide, Tf2N-) or methanesulfonate (mesylate, OMs-) anions were synthesized and characterized. The chain length of the alkyl side chain on the imidazole ligand was varied. All compounds were characterized using CHN analysis, DSC and FTIR measurements. Single-crystal X-ray diffraction measurements were performed on six of the compounds for which single crystals of good quality could be obtained. All cobalt(ii) centers are six-coordinate with the N-alkylimidazole ligands in an octahedral configuration and the anions are non-coordinating. The same coordination environment was observed by EXAFS measurements on cobalt(ii) liquid metal salts in the liquid state. The electrochemical properties of the compounds with the lowest melting temperatures were investigated using cyclic voltammetry. It was found that part of the current was consumed in the electrodeposition of cobalt, whereas the other part of the current was consumed in the electrochemical formation of cobalt(0) nanoparticles.

Manganese-containing ionic liquids: synthesis, crystal structures and electrodeposition of manganese films and nanoparticles.

Manganese(ii)-containing ionic liquids were synthesized, in which the manganese atoms are coordinated by glymes (diglyme, triglyme, tetraglyme), pyridine-N-oxide, dimethylsulfoxide or N-alkylimidazoles (N-methylimidazole, N-butylimidazole and N-hexylimidazole). As anion, bis(trifluoromethanesulfonyl)imide (bistriflimide, Tf2N-), trifluoromethanesulfonate (triflate, OTf-) or methanesulfonate (mesylate, OMs-) were used. The compounds were characterized by CHN analysis, FTIR, DSC and single-crystal X-ray diffraction measurements. All manganese atoms were six-coordinate. It was found that the glyme-type ligands were replaced by atmospheric water upon leaving the crystals open to the air for several days. The crystal structures of seven compounds were described in detail and the compounds with the lowest melting temperatures were tested as electrolytes for the electrodeposition of manganese (thin) films. An irreversible reduction wave from Mn(ii) to Mn(0) and granular manganese deposits were observed for all compounds, except for liquid manganese salts with N-alkylimidazole ligands and bistriflimide anions, where the electrochemical formation of manganese nanoparticles was observed instead of the deposition of a manganese layer. However, for compounds with the same cation but with a triflate or methanesulfonate anion, manganese metal deposits were obtained, indicating that the nature of the anion has an important effect on the electrochemical properties of liquid metal salts.

Deliberate and Accidental Gas-Phase Alkali Doping of Chalcogenide Semiconductors: Cu(In,Ga)Se2.

Alkali metal doping is essential to achieve highly efficient energy conversion in Cu(In,Ga)Se2 (CIGSe) solar cells. Doping is normally achieved through solid state reactions, but recent observations of gas-phase alkali transport in the kesterite sulfide (Cu2ZnSnS4) system (re)open the way to a novel gas-phase doping strategy. However, the current understanding of gas-phase alkali transport is very limited. This work (i) shows that CIGSe device efficiency can be improved from 2% to 8% by gas-phase sodium incorporation alone, (ii) identifies the most likely routes for gas-phase alkali transport based on mass spectrometric studies, (iii) provides thermochemical computations to rationalize the observations and (iv) critically discusses the subject literature with the aim to better understand the chemical basis of the phenomenon. These results suggest that accidental alkali metal doping occurs all the time, that a controlled vapor pressure of alkali metal could be applied during growth to dope the semiconductor, and that it may have to be accounted for during the currently used solid state doping routes. It is concluded that alkali gas-phase transport occurs through a plurality of routes and cannot be attributed to one single source.

High-speed electrodeposition of copper-tin-zinc stacks from liquid metal salts for Cu2ZnSnSe4 solar cells.

Cu2ZnSnSe4-based solar cells with 5.5% power conversion efficiency were fabricated from Cu/Sn/Zn stacks electrodeposited from liquid metal salts. These electrolytes allow metal deposition rates one order of magnitude higher than those of other deposition methods.

Severe ischemic colitis following olanzapine use - A case report.

Ischemic colitis is the most common subtype of intestinal ischemia usually resulting from vasospasm, vessel occlusion or mesenteric hypoperfusion. Neuroleptics have seldom been linked to ischemic colitis by blocking peripheral anticholinergic and antiserotonergic receptors inducing severe gastrointestinal paresis. We report a young patient with severe ischemic colitis requiring surgery due to necrosis of the bowel. After exclusion of other potential causes, olanzapine was admitted as the cause of ischemia. Clinicians should be aware of how to recognize and treat the potentially life-threatening effects of neuroleptics.

Tuning the gallium content of metal precursors for Cu(In,Ga)Se2 thin film solar cells by electrodeposition from a deep eutectic solvent.

Controlling the Ga incorporation of Cu-In-Ga metal precursors for Cu(In,Ga)Se2 (CIGS) solar cells is one of the main challenges for low cost electrodeposition processes, mainly due to the difficulty in electrodepositing metallic Ga from aqueous electrolytes. In this work we use the deep eutectic solvent (DES) Choline Chloride : Urea (ChCl : U - 1 : 2) to efficiently codeposit In-Ga on Cu and Mo electrodes. We control the Ga/(Ga+In) (Ga/III) ratio of the films via the mass fluxes. The electrochemical behavior of ChCl : U containing GaCl3 and InCl3 is studied by rotating disk electrode cyclic voltammetry (CV) on Mo and Cu electrodes. CV revealed on both Mo and Cu electrodes that the electrochemical behavior of the ChCl : U-GaCl3-InCl3 system is the superposition of the individual In and Ga electrochemistry. On a Cu electrode the morphology, crystal structure and element distribution of the deposits were a function of the Ga/III ratio. We demonstrate the precise control of Ga incorporation over a large composition range from 0.1 ≤ Ga/III ≤ 0.9 and proved that ED from DES is a straightforward, robust and efficient process. First solar cells based on Mo/Cu/In-Ga metal stacks achieved efficiencies as high as 7.9% with a Voc of 520 mV.